I could just list individual stages and such, but instead I'll just detail my likes/dislikes from each game.
EoSD:
Besides Apparitions Stalk the Night, all songs Pre-Stage 4, as well as stage themes for 4,6 and EX, are a bit on my dislike list. Beloved Tomboyish Daughter would also be an exception, but I mostly like the remixes for that theme. The Locked Girl, Septette for the Dead Princess, and U.N. Owen are some of my favorites, with Lunar Clock Lunar Dial being my absolute fave. I blame the fact I like a bit of metal/rock in my Touhou.
PCB:
Most of the songs in this game are enjoyable to me, probably because it was the first Touhou game I ever played. I honestly think that every song in this game is not hated by me in any way, though my most favorite would have to be Phantom Ensemble. I think I have soft spot for songs that have violins in them. Some songs like the Stage 1 theme, Stage 2, and Chen's boss theme aren't the best but they are enjoyable.
IN
In all honesty, this ranks 3rd on my least favorite in terms of games. To me, if I can remember how a theme goes, it means I like it. While trying to recall themes, IN was probably the one that I least remembered without having to replay it. Mystia's stage and boss theme is definitely one of my favorites though, with Love Coloured Master Spark, Cinderella Cage, and Gensokyo Millenium also being up there. Most of the other songs though just aren't too good for me.
IN
Since most of it is just remixes I can't really comment much about it.
PoFV
Similar to IN, though I will say that the music was somewhat terrible. While a few gems were there(Higan Retour, and Fate of the Sixtieth Year..was that what it was?I forgot), most of the other songs just made me wanna mute the computer. And about Youmu's theme...completely agree! Till When should of been used instead of something I could fall asleep to.
StB
This game had music?
MoF
This one ranks number one on my least favorite. While having more songs that I like compared to PoFV, the music in most of the game was just extremely lackluster. While I didn't give much of an eye to Nitori's theme, after hearing a certain vocal version, I started liking it a little bit more. Fall of Falls~Autumn Waterfall, Faith is for the Transient People and The Venerable Ancient Battlefield are the only themes I like in this game. Everything else just disappoints me.
SWR
Similar to IaMP, but Tenshi's theme and Reisen's remix are pretty good.
SA
1st stage is good, boss theme is okay, 2nd stage is good, boss is okay, 3rd stage is okay, boss is good, 4th stage is okay, boss is amazing, 5th stage is okay, boss is good, 6th stage is not so good, boss is great. I know I'm not going too well into this one, but it doesn't stand out too well, but it's not that bad. It's 4th on my least favorite though.
UNL
Faith is for the Transient People remix is nice, but the others aren't too nice. Well Solar Sect of Mystic Wisdom is nice here too.
UFO
Had some of my favorite songs here. Beware the Umbrella Left There Forever, Captain Murasa, The Tiger Patterned...Shou's theme..Emotional Skyscraper - Cosmic Mind, UFO Romance in the Night(I think that's what it is), and Heian Alien are all my favorites. I can't stop listening to these songs really.
PC-98 games
Of all the games, I only know 3 themes(Well 4 if Yuka's is from this series of games and not just PoFV). These include Reincarnation, Bad Apple, and Complete Darkness. The first two are my most favorite from the PC-98 series while the last one I only heard while looking for remixes for Reincarnation. It was ok, but not my favorite.